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In Progress
Clinical

Dataset with samples from Individuals with:

A- Defects in Intrinsic and Innate Immunity:

1)- TLR signaling pathway deficiency: MyD88 deficiency, Phenotype OMIM number 612260

B- Combined immunodeficiencies with associated or syndromic features:

1)- HOLI1/RBCK1 deficiency, Phenotype OMIM number 615895

2)- Anhidrotic ectodermalsysplasia with immunodeficiencies: NEMO deficiency, Phenotype OMIM number 300291

see PID classification: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4659841/

Purpose

Loss-of-expression and loss-of-function mutations in HOIL1 (RBCK1) results in disruption of the linear ubiquitination assembly complex (LUBAC). Impairment of LUBAC results in impaired NF-kB activation in response to TNF and IL-1b in fibroblastic cells, but also display enhanced pro-inflammatory responses to TNF and IL-1b in leukocytes. Autosomal recessive complete human HOIL-1/RBCK1 deficiency is a new disorder with unbalanced cellular responses to pro-inflammatory cytokines, resulting in the paradoxical association of auto-inflammation and pyogenic bacterial disease, as well as the surprising development of muscular amylopectinosis. The genome-wide gene expression analysis showed that human HOIL-1 deficiency results in impaired NF-B activation in response to TNF- and IL-1 in fibroblastic cells.

Hypothesis

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Experimental Design

Skin fibroblast cell lines were derived from controls (n=3), patients with deficiencies for RBCK1 (HOIL1) (n=2), MYD88 (n=1), and NEMO (n=1). Cells were cultured for 8 or 24 hours in the presence of TNF (5ng/ml) or IL1B (5ng/ml) or left unstimulated for the same length of time.

Experimental Variables

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Controls

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Methods

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Additional Information

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Microarray
Illumina HumanHT-12 v4
46 Samples Loaded: 46
Human (Homo sapiens)
Fibroblast
HOIL1/RBCK1 deficiency, MyD88 deficiency, NEMO deficiency
Sample Set Spreadsheet
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Samples Preview
Sample ID !Sample Title group Cell type treatment Disease type
GSM769312 Ctrl1 TNF 8h Control TNF 8h fibroblast 5ng/ml TNF healthy control
GSM769313 RBCK1-/- 1 IL1B 8h AR RBCK1 IL1B 8h fibroblast 5ng/ml IL1B RBCK1 deficient patient
GSM769314 Ctrl1 TNF 24h Control TNF 24h fibroblast 5ng/ml TNF healthy control
GSM769315 RBCK1-/- 2 NS 8h AR RBCK1 NS 8h fibroblast Non-stimulated RBCK1 deficient patient
GSM769316 RBCK1-/- 2 IL1B 24h AR RBCK1 IL1B 24h fibroblast 5ng/ml IL1B Fibroblasts RBCK1 deficient patient
Please log in in order to upload files.
File
sampleset4000032_sampleannotations_Group.csv
Sample Set Spreadsheet
sampleset4000032_sampleannotations_Group.csv
Sample Set Spreadsheet
sampleset4000032_sampleannotations_Group.csv
Sample Set Spreadsheet
Raw Signal
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Samples Viewer / Editor

All fields are editable except the "Sample ID" column. To edit a cell, click within the cell. To edit a "date" cell, click on the calendar icon. To cancel an edit, press the ESC key.

Sample ID !Sample Title Group Cell type Treatment Disease type Time (hours)
GSM769312
Ctrl1 TNF 8h
Control TNF 8h
fibroblast
5ng/ml TNF
healthy control
8
GSM769313
RBCK1-/- 1 IL1B 8h
AR RBCK1 IL1B 8h
fibroblast
5ng/ml IL1B
RBCK1 deficient patient
8
GSM769314
Ctrl1 TNF 24h
Control TNF 24h
fibroblast
5ng/ml TNF
healthy control
24
GSM769315
RBCK1-/- 2 NS 8h
AR RBCK1 NS 8h
fibroblast
Non-stimulated
RBCK1 deficient patient
8
GSM769316
RBCK1-/- 2 IL1B 24h
AR RBCK1 IL1B 24h
fibroblast
5ng/ml IL1B
Fibroblasts RBCK1 deficient patient
24
GSM769317
Ctrl1 NS 24h
Control NS 24h
fibroblast
Non-stimulated
healthy control
24
GSM769318
Ctrl6 NS 8h
Control NS 8h
fibroblast
Non-stimulated
healthy control
8
GSM769319
Ctrl6 IL1B 8h
Control IL1B 8h
fibroblast
5ng/ml IL1B
healthy control
8
GSM769320
RBCK1-/- 1 IL1B 24h
AR RBCK1 IL1B 24h
fibroblast
5ng/ml IL1B
RBCK1 deficient patient
24
GSM769321
Ctrl5 IL1B 8h
Control IL1B 8h
fibroblast
5ng/ml IL1B
healthy control
8
GSM769322
Ctrl5 NS 24h
Control NS 24h
fibroblast
Non-stimulated
healthy control
24
GSM769323
RBCK1-/- 2 TNF 24h
AR RBCK1 TNF 24h
fibroblast
5ng/ml TNF
RBCK1 deficient patient
24
GSM769324
Ctrl1 NS 8h
Control NS 8h
fibroblast
Non-stimulated
healthy control
8
GSM769325
Nemo-/- TNF 8h
AR NEMO TNF 8h
fibroblast
5ng/ml TNF
NEMO deficient patient
8
GSM769326
RBCK1-/- 1 TNF 24h
AR RBCK1 TNF 24h
fibroblast
5ng/ml TNF
RBCK1 deficient patient
24
GSM769327
Nemo-/- IL1B 8h
AR NEMO IL1B 8h
fibroblast
5ng/ml IL1B
NEMO deficient patient
8
GSM769328
Nemo-/- NS 24h
AR NEMO NS 24h
fibroblast
Non-stimulated
NEMO deficient patient
24
GSM769329
RBCK1-/- 1 TNF 8h
AR RBCK1 TNF 8h
fibroblast
5ng/ml TNF
RBCK1 deficient patient
8
GSM769330
Myd88-/- IL1B 8h
AR MyD88 IL1B 8h
fibroblast
5ng/ml IL1B
MyD88 deficient patient
8
GSM769331
RBCK1-/- 2 TNF 8h
AR RBCK1 TNF 8h
fibroblast
5ng/ml TNF
RBCK1 deficient patient
8
GSM769332
Myd88-/- NS 24h
AR MyD88 NS 24h
fibroblast
Non-stimulated
MyD88 deficient patient
24
GSM769333
RBCK1-/- 1 NS 8h
AR RBCK1 NS 8h
fibroblast
Non-stimulated
RBCK1 deficient patient
8
GSM769334
Ctrl1 IL1B 8h
Control IL1B 8h
fibroblast
5ng/ml IL1B
healthy control
8
GSM769335
Nemo-/- NS 8h
AR NEMO NS 8h
fibroblast
Non-stimulated
NEMO deficient patient
8
GSM769336
RBCK1-/- 1 NS 24h
AR RBCK1 NS 24h
fibroblast
Non-stimulated
RBCK1 deficient patient
24
GSM769337
Nemo-/- IL1B 24h
AR NEMO IL1B 24h
fibroblast
5ng/ml IL1B
NEMO deficient patient
24
GSM769338
Ctrl5 IL1B 24h
Control IL1B 24h
fibroblast
5ng/ml IL1B
healthy control
24
GSM769339
Ctrl5 NS 8h
Control NS 8h
fibroblast
Non-stimulated
healthy control
8
GSM769340
Nemo-/- TNF 24h
AR NEMO TNF 24h
fibroblast
5ng/ml TNF
NEMO deficient patient
24
GSM769341
Ctrl6 IL1B 24h
Control IL1B 24h
fibroblast
5ng/ml IL1B
healthy control
24
GSM769342
Ctrl5 TNF 24h
Control TNF 24h
fibroblast
5ng/ml TNF
healthy control
24
GSM769343
Myd88-/- IL1B 24h
AR MyD88 IL1B 24h
fibroblast
5ng/ml IL1B
MyD88 deficient patient
24
GSM769344
Ctrl6 TNF 24h
Control TNF 24h
fibroblast
5ng/ml TNF
healthy control
24
GSM769345
Ctrl6 NS 24h
Control NS 24h
fibroblast
Non-stimulated
healthy control
24
GSM769346
RBCK1-/- 2 NS 24h
AR RBCK1 NS 24h
fibroblast
Non-stimulated
RBCK1 deficient patient
24
GSM769347
Myd88-/- NS 8h
AR MyD88 NS 8h
fibroblast
Non-stimulated
MyD88 deficient patient
8
GSM769348
RBCK1-/- 2 IL1B 8h
AR RBCK1 IL1B 8h
fibroblast
5ng/ml IL1B
RBCK1 deficient patient
8
GSM769349
Ctrl1 IL1B 24h
Control IL1B 24h
fibroblast
5ng/ml IL1B
healthy control
24
GSM769350
Myd88-/- TNF 24h
AR MyD88 TNF 24h
fibroblast
5ng/ml TNF
MyD88 deficient patient
24
GSM769351
Myd88-/- TNF 8h
AR MyD88 TNF 8h
fibroblast
5ng/ml TNF
MyD88 deficient patient
8
GSM769352
Ctrl5 TNF 8h
Control TNF 8h
fibroblast
5ng/ml TNF
healthy control
8
GSM769353
Ctrl6 TNF 8h
Control TNF 8h
fibroblast
5ng/ml TNF
healthy control
8
GSM769354
Ctrl1 TNF 24h rep2
Control TNF 24h
fibroblast
5ng/ml TNF
healthy control
24
GSM769355
Ctrl1 NS 24h rep2
Control NS 24h
fibroblast
Non-stimulated
healthy control
24
GSM769356
Myd88-/- NS 24h rep2
AR MyD88 NS 24h
fibroblast
Non-stimulated
MyD88 deficient patient
24
GSM769357
Nemo-/- TNF 24h rep2
AR NEMO TNF 24h
fibroblast
5ng/ml TNF
NEMO deficient patient
24

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